YRFG_ECOLI
ID YRFG_ECOLI Reviewed; 222 AA.
AC P64636; P45801; Q2M764;
DT 11-OCT-2004, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=GMP/IMP nucleotidase YrfG;
DE EC=3.1.3.5;
GN Name=yrfG; OrderedLocusNames=b3399, JW5865;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [3]
RP FUNCTION AS A PURINE NUCLEOTIDASE, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE
RP SPECIFICITY, AND COFACTOR.
RX PubMed=16990279; DOI=10.1074/jbc.m605449200;
RA Kuznetsova E., Proudfoot M., Gonzalez C.F., Brown G., Omelchenko M.V.,
RA Borozan I., Carmel L., Wolf Y.I., Mori H., Savchenko A.V., Arrowsmith C.H.,
RA Koonin E.V., Edwards A.M., Yakunin A.F.;
RT "Genome-wide analysis of substrate specificities of the Escherichia coli
RT haloacid dehalogenase-like phosphatase family.";
RL J. Biol. Chem. 281:36149-36161(2006).
CC -!- FUNCTION: Catalyzes the dephosphorylation of different purine
CC nucleotides (GMP and IMP). Also hydrolyzes flavin mononucleotide (FMN).
CC {ECO:0000269|PubMed:16990279}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-phosphate + H2O = a ribonucleoside +
CC phosphate; Xref=Rhea:RHEA:12484, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:18254, ChEBI:CHEBI:43474, ChEBI:CHEBI:58043; EC=3.1.3.5;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:16990279};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:16990279};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:16990279};
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:16990279};
CC Note=Magnesium. Can also use other divalent metal cations as manganese,
CC cobalt or zinc. {ECO:0000269|PubMed:16990279};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.010 mM for IMP (with manganese ions as cofactor and at pH 9)
CC {ECO:0000269|PubMed:16990279};
CC KM=0.012 mM for GMP (with manganese ions as cofactor and at pH 9)
CC {ECO:0000269|PubMed:16990279};
CC KM=0.062 mM for GMP (with magnesium ions as cofactor and at pH 9)
CC {ECO:0000269|PubMed:16990279};
CC KM=0.22 mM for IMP (with magnesium ions as cofactor and at pH 9)
CC {ECO:0000269|PubMed:16990279};
CC pH dependence:
CC Optimum pH is between 6 and 7.5. {ECO:0000269|PubMed:16990279};
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA58196.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; U18997; AAA58196.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC76424.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE77892.1; -; Genomic_DNA.
DR PIR; B65135; B65135.
DR RefSeq; NP_417858.4; NC_000913.3.
DR RefSeq; WP_001295168.1; NZ_STEB01000004.1.
DR AlphaFoldDB; P64636; -.
DR SMR; P64636; -.
DR BioGRID; 4260978; 19.
DR STRING; 511145.b3399; -.
DR PaxDb; P64636; -.
DR PRIDE; P64636; -.
DR EnsemblBacteria; AAC76424; AAC76424; b3399.
DR EnsemblBacteria; BAE77892; BAE77892; BAE77892.
DR GeneID; 66672721; -.
DR GeneID; 947904; -.
DR KEGG; ecj:JW5865; -.
DR KEGG; eco:b3399; -.
DR PATRIC; fig|1411691.4.peg.3331; -.
DR EchoBASE; EB2764; -.
DR eggNOG; COG1011; Bacteria.
DR HOGENOM; CLU_106706_0_0_6; -.
DR InParanoid; P64636; -.
DR OMA; HDYGFPK; -.
DR PhylomeDB; P64636; -.
DR BioCyc; EcoCyc:G7742-MON; -.
DR BioCyc; MetaCyc:G7742-MON; -.
DR PRO; PR:P64636; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0050484; F:GMP 5'-nucleotidase activity; IDA:EcoCyc.
DR GO; GO:0050483; F:IMP 5'-nucleotidase activity; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
DR GO; GO:0008967; F:phosphoglycolate phosphatase activity; IBA:GO_Central.
DR GO; GO:0008477; F:purine nucleosidase activity; IDA:EcoliWiki.
DR GO; GO:0106411; F:XMP 5'-nucleosidase activity; IEA:UniProtKB-EC.
DR GO; GO:0016311; P:dephosphorylation; IDA:EcoliWiki.
DR GO; GO:0006281; P:DNA repair; IBA:GO_Central.
DR Gene3D; 3.40.50.1000; -; 1.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006439; HAD-SF_hydro_IA.
DR InterPro; IPR041492; HAD_2.
DR InterPro; IPR023214; HAD_sf.
DR Pfam; PF13419; HAD_2; 1.
DR PRINTS; PR00413; HADHALOGNASE.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01509; HAD-SF-IA-v3; 1.
PE 1: Evidence at protein level;
KW Hydrolase; Magnesium; Manganese; Metal-binding; Reference proteome.
FT CHAIN 1..222
FT /note="GMP/IMP nucleotidase YrfG"
FT /id="PRO_0000169542"
FT ACT_SITE 9
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT BINDING 9..11
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 9
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 11
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 149
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 174
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
SQ SEQUENCE 222 AA; 25399 MW; AC2AB3BCFE779491 CRC64;
MHINIAWQDV DTVLLDMDGT LLDLAFDNYF WQKLVPETWG AKNGVTPQEA MEYMRQQYHD
VQHTLNWYCL DYWSEQLGLD ICAMTTEMGP RAVLREDTIP FLEALKASGK QRILLTNAHP
HNLAVKLEHT GLDAHLDLLL STHTFGYPKE DQRLWHAVAE ATGLKAERTL FIDDSEAILD
AAAQFGIRYC LGVTNPDSGI AEKQYQRHPS LNDYRRLIPS LM
